DNA Sequence Alignment

Sequence alignment visualization and editing. Annotations. Select from multiple algorithms.

Awesome sequence alignment visualization and editing
  • Show annotations on the alignment and edit at the same time
  • Drag to remove or insert gaps
  • Join sequences together
  • Strip columns
  • Type directly into an alignment
  • Correct bad calls
  • Viewing and coloring by translation alongside allows you to correct coding sequences
  • View phylogeny alongside the alignment and link back to a tree
  • Similarity and sequence logo graphs
  • Real-time updates to the statistics panel (real-time) update according to selection
  • Spot disagreements easily with highlighting
Access a variety of DNA alignments including Clustal Omega, MUSCLE and MAFFT from within one software program

Save time and stop jumping around from program to program. Select a specific task to perform without leaving Geneious. Built in alignments include:

  • The Geneious Aligner
  • Clustal Omega
  • Local Re-alignment
  • Pairwise alignment
  • Translation Align
  • Consensus Align
  • MAFFT- available as a plugin
  • MAUVE- available as a plugin
  • LastZ – available as plugin
Your data your way

No matter what alignment you choose, the data is still yours to edit and annotate in a way that works for you.

Better genome alignments are just a few clicks away.




Phylogenetic Trees

Build phylogenetic trees using peer-reviewed algorithms, including RAxML and PAUP*

Assembly and Mapping

De novo assembly or reference mapping using industry leading algorithms, including TopHat and Velvet.

Sanger Sequencing

Trim, assemble, and view Sanger sequencing trace files. Powerful SNP detection and variant calling.

Import Data

Import and convert common file types as well as their annotations and notes with a simple drag and drop


How to build phylogenetic trees
How to perform de novo assembly
How to perform Sanger Sequencing
Quick Start to Geneious Prime
Geneious is paramount in my research so I can’t be without it for too long.
Bob LitermanIowa State University